Metabolic Engineering of Corynebacterium glutamicum for the High-Level Production of l-Valine under Aerobic Conditions.

l-Valine, an essential amino acid, serves as a valuable compound in various industries. However, engineering strains with both high yield and purity are yet to be delivered for microbial l-valine production. We engineered a Corynebacterium glutamicum strain capable of highly efficient production of l-valine. We initially introduced an acetohydroxy acid synthase mutant from an industrial l-valine producer and optimized a cofactor-balanced pathway, followed by the activation of the nonphosphoenolpyruvate-dependent carbohydrate phosphotransferase system and the introduction of an exogenous Entner-Doudoroff pathway. Subsequently, we weakened anaplerotic pathways, and attenuated the tricarboxylic acid cycle via start codon substitution in icd, encoding isocitrate dehydrogenase. Finally, to balance bacterial growth and l-valine production, an l-valine biosensor-dependent genetic circuit was established to dynamically repress citrate synthase expression. The engineered strain Val19 produced 103 g/L of l-valine with a high yield of 0.35 g/g glucose and a productivity of 2.67 g/L/h. This represents the highest reported l-valine production in C. glutamicum via direct fermentation and exhibits potential for its industrial-scale production, leveraging the advantages of C. glutamicum over other microbes.

Large Flux Supply of NAD(H) under Aerobic Conditions by Candida glycerinogenes.

NAD is a redox coenzyme and is the center of energy metabolism. In metabolic engineering modifications, an insufficient NAD(H) supply often limits the accumulation of target products. In this study, Candida glycerinogenes was found to be able to supply NAD(H) in large fluxes, up to 7.6 times more than Saccharomyces cerevisiae in aerobic fermentation. Aerobic fermentation in a medium without amino nitrogen sources demonstrated that C. glycerinogenes NAD synthesis was not dependent on NAD precursors in the medium. Inhibition by antisense RNA and the detection of transcript levels indicated that the main NAD supply pathway is the de novo biosynthesis pathway. It was further demonstrated that NAD(H) supply was unaffected by changes in metabolic flow through C. glycerinogenes ΔGPD aerobic fermentation (80 g/L ethanol). In conclusion, the ability of C. glycerinogenes to supply NAD(H) in large fluxes provides a new approach to solving the NAD(H) supply problem in synthetic biology.

Humic acid biosynthesis and bacterial community evolution during aerobic composting of rice straw.

In this study, the effects of inoculum ratio, substrate particle size and aeration rate on humic acid (HA) biosynthesis during aerobic composting of rice straw were investigated, respectively. The contents of total organic carbon, total nitrogen and HA, as well as lignocellulose degradation in the composting were evaluated, respectively. It is found that the maximal HA yield of 356.9 g kg-1 was obtained at an inoculum ratio of 20%, a substrate particle size of 0.83 mm and an aeration rate of 0.3 L·kg-1 DM min-1 in the process of composting. The changes of microbial communities and metabolic functions at different stages of the composting were also analyzed through high-throughput sequencing. The result demonstrates that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the dominant phyla and their relative abundance significantly varied over time (p < 0.05), and Rhizobium, Phenylobacterium, Pseudoxanthomonas and Paenibacillus were positively related to HA content in the compost. Furthermore, the metabolic function profiles of bacterial community indicate that these functional genes in carbohydrate metabolism and amino acid metabolism were involved in lignocellulose biodegradation and HA biosynthesis. This work may be conducive to explore new regulation strategy to improve bioconversion efficiency of agricultural residues to applicable biofertilizers. KEY POINTS: • Temperature, pH, TOC, TN and C/N caused a great influence on humic acids synthesis • The succession of the microbial community during the composting were evaluated • The metabolisms of carbohydrate and amino acids were involved in HA synthesis.

Co-composting of sewage sludge as an effective technology for the production of substrates with reduced content of pharmaceutical residues.

Sewage sludge is a valuable source of elements such as phosphorus and nitrogen. At the same time, heavy metals, emerging organic compounds, micropollutants (pharmaceuticals, pesticides, PCPs, microplastics), or some potentially dangerous bacteria can be present. In this study, the sewage sludge was aerobically treated by composting with other materials (co-composted), and the resulting substrate was tested for suitability of its use in agriculture. Closer attention was focused on the pharmaceuticals (non-steroidal antiphlogistics, sartanes, antiepileptics, caffeine, and nicotine metabolites) content and ecotoxicity of the resulting substrates in the individual phases of sludge co-composting. It has been verified that during co-composting there is a potential for reduction of the content of pharmaceutical in the substrates up to 90 %. The course of the temperature in the thermophilic phase is decisive. Growth and ecotoxicity experiments demonstrated that with a suitable co-composting procedure, the resulting stabilized matter is suitable as a substrate for use in plant production, and the risk of using sewage sludge on agricultural land is substantially reduced.

A role for fermentation in aerobic conditions as revealed by computational analysis of maize root metabolism during growth by cell elongation.

The root is a well-studied example of cell specialisation, yet little is known about the metabolism that supports the transport functions and growth of different root cell types. To address this, we used computational modelling to study metabolism in the elongation zone of a maize lateral root. A functional-structural model captured the cell-anatomical features of the root and modelled how they changed as the root elongated. From these data, we derived constraints for a flux balance analysis model that predicted metabolic fluxes of the 11 concentric rings of cells in the root. We discovered a distinct metabolic flux pattern in the cortical cell rings, endodermis and pericycle (but absent in the epidermis) that involved a high rate of glycolysis and production of the fermentation end-products lactate and ethanol. This aerobic fermentation was confirmed experimentally by metabolite analysis. The use of fermentation in the model was not obligatory but was the most efficient way to meet the specific demands for energy, reducing power and carbon skeletons of expanding cells. Cytosolic acidification was avoided in the fermentative mode due to the substantial consumption of protons by lipid synthesis. These results expand our understanding of fermentative metabolism beyond that of hypoxic niches and suggest that fermentation could play an important role in the metabolism of aerobic tissues.

Novelty three stages for humification of sewage sludge during hyperthermophilic aerobic fermentation.

Compared with conventional aerobic fermentation (CAF), there is limited knowledge of how hyperthermophilic aerobic fermentation (HAF) enhances the humification of sewage sludge. This study compared three novel stages of organic degradation, precursors, functional groups, bacterial community, and humus synthesis mechanism in HAF with CAF. The results showed that organic matter (OM) degraded rapidly, and 68% of the degradation could be completed of stage I in HAF. Compared with the initial stage, ammonium nitrogen (NH4+-N), water-soluble organic carbon, and water-soluble total nitrogen increased by 2.83 times, 40.5 times, and 33.5 times, respectively. Cellulose and hemicellulose decreased by 29.22% and 21.85%, respectively. These results suggested that temperature (>80 °C) and Bacillus dominated accelerate the humification process by rapidly improving OM degradation. Compared with the initial value of HAF, the maximum increment of reducing sugar at stage II was 297%, and the degradation rate of cellulose was effectively increased by 21.03% compared with that of CAF. The precursors such as reducing sugars and amino acids formed humus at stage II. The content of Aryl C increased significantly during the HAF process, the degree of polymerization of humus and the aromatization degree of HA and FA increased significantly, and complex organic macromolecular material polymers were formed at stage III. The sugar-amine condensation was the mechanism of humification in the sludge HAF process. This investigation provided three new stages of insights into the synthesis of humification during the HAF process and extended the current mechanism of humification in the HAF process.

The transformation of heavy metal speciation during rapid high-temperature aerobic fermentation of food waste and their potential mechanisms.

In this study, the content changes of multiple trace heavy metals (HMs) in food waste using a new rapid high-temperature aerobic fermentation (RTAF) technology and their relationships with different physicochemical factors were researched. The results indicated that the content of HMs in the decomposed products met the industry standards for organic fertilizers (NY/T525-2021, China). Physicochemical factors played an important role in controlling the changes in HM content. The component evolution of dissolved organic matter was studied, and its influences on the transformation of HM speciation showed that the RTAF process converted proteins into humus-like substances. Redundancy analysis revealed that the main factors driving the speciation transformation of HMs were tyrosine-like substances or microbial-derived humus (C3), molecular weight of dissolved organic matter (SUVA254) and humification degree (E250/E365). The increase in humification degree contributed to passivating HMs. The correlation network analysis results showed that the exchangeable HMs (Exc-HMs) were related to Lactobacillus and Pediococcu. Additionally, the cytoskeleton, coenzyme transport and metabolic function of microorganisms affected the Exc-HM content. These research results can provide a scientific basis for the prevention and control of HM pollution during the treatment of food waste.

Reduction of ethanol content in wine with an improved combination of yeast strains and process conditions.

One interesting strategy to address the increasing alcohol content of wines, associated with climate change, is to reduce the ethanol yield during fermentation. Within this strategy, the approach that would allow the clearest reduction in alcohol content is the respiration of part of the grape sugars by yeasts. Non-Saccharomyces species can be used for this purpose but suffer from a limited ability to dominate the process and complete fermentation. In turn, Saccharomyces cerevisiae shows a high production of acetic acid under the growth conditions required for respiration. Previously proposed procedures used combinations of non-Saccharomyces and S. cerevisiae starters, or a strain of S. cerevisiae (PR1018), with unique metabolic properties. In both cases, precise management of oxygen availability was required to overcome the acetic acid problem. In this work, we have developed a laboratory scale process to take advantage of the properties of PR1018 and a strain of Metschnikowia pulcherrima. This process is more robust than the previous ones and does not rely on strict control of oxygenation or even the use of this particular strain of S. cerevisiae. Aeration can be interrupted instantly without impairing the volatile acidity. Under the selected conditions, an ethanol reduction of around 3% (v/v) was obtained compared to the standard fermentation control.

Fermentation-mediated growth, signaling, and defense in plants.

While traditionally considered important mainly in hypoxic roots during flooding, upregulation of fermentation pathways in plants has recently been described as an evolutionarily conserved drought survival strategy, with acetate signaling mediating reprograming of transcription and cellular carbon and energy metabolism from roots to leaves. The amount of acetate produced directly correlates with survival through potential mechanisms including defense gene activation, biosynthesis of primary and secondary metabolites, and aerobic respiration. Here, we review root ethanolic fermentation responses to hypoxia during saturated soil conditions and summarize studies highlighting acetate fermentation under aerobic conditions coupled with respiration during growth and drought responses. Recent work is discussed demonstrating long-distance transport of acetate via the transpiration stream as a respiratory substrate. While maintenance and growth respiration are often modeled separately in terrestrial models, here we propose the concept of 'Defense Respiration' fueled by acetate fermentation in which upregulation of acetate fermentation contributes acetate substrate for alternative energy production via aerobic respiration, biosynthesis of primary and secondary metabolites, and the acetylation of proteins involved in defense gene regulation. Finally, we highlight new frontiers in leaf-atmosphere emission measurements as a potential way to study acetate fermentation responses of individual leaves, branches, ecosystems, and regions.

Directed evolution of Saccharomyces cerevisiae for low volatile acidity during winemaking under aerobic conditions.

The use of yeast respiratory metabolism has been proposed as a promising approach to solve the problem of increasing ethanol content in wine, which is largely due to climate change. The use of S. cerevisiae for this purpose is mostly hampered by acetic acid overproduction generated under the necessary aerobic conditions. However, it was previously shown that a reg1 mutant, alleviated for carbon catabolite repression (CCR), showed low acetic acid production under aerobic conditions. In this work directed evolution of three wine yeast strains was performed to recover CCR-alleviated strains, expecting they will also be improved concerning volatile acidity. This was done by subculturing strains on galactose, in the presence of 2-deoxyglucose for around 140 generations. As expected, all evolved yeast populations released less acetic acid than their parental strains in grape juice, under aerobic conditions. Single clones were isolated from the evolved populations, either directly or after one cycle of aerobic fermentation. Only some clones from one of three original strains showed lower acetic acid production than their parental strain. Most clones isolated from EC1118 showed slower growth. However, even the most promising clones failed to reduce acetic acid production under aerobic conditions in bioreactors. Therefore, despite the concept of selecting low acetic acid producers by using 2-deoxyglucose as selective agent was found to be correct, especially at the population level, the recovery of strains with potential industrial utility by this experimental approach remains a challenge.

Kinetic model derivation for design, building and operation of solid waste treatment unit based on system dynamics and computer simulation.

Solid waste disposal is significantly important to maintaining normal operation of both natural and artificial ecosystems. In this study, a kinetic model of solid waste treatment unit (SWTU) was upfront developed based on microbial ecology, system dynamics, cybernetics and digital simulation, which accurately described the relationships and interactions between solid waste decomposition (SWD) processes and biotic/abiotic factors. Then a specific SWTU prototype was designed and built from this kinetic model. A 370-day experiment demonstrated that SWTU maintained normal operation with robust stability and desired dynamic behaviors, and effectively disposed the solid waste. Therefore, this kinetic model was highly valid due to its high structural and behavioral similarity with the prototype. This research could lay a strong theoretical foundation for further closed-loop control as well as optimization of SWTU, and provide scientific guidance to environmental management as well as sustainable development.

The Warburg effect: a signature of mitochondrial overload.

A long-standing question in cancer biology has been why oxygenated tumors ferment the majority of glucose they consume to lactate rather than oxidizing it in their mitochondria, a phenomenon known as the 'Warburg effect.' An abundance of evidence shows not only that most cancer cells have fully functional mitochondria but also that mitochondrial activity is important to proliferation. It is therefore difficult to rationalize the metabolic benefit of cancer cells switching from respiration to fermentation. An emerging perspective is that rather than mitochondrial metabolism being suppressed in tumors, as is often suggested, mitochondrial activity increases to the level of saturation. As such, the Warburg effect becomes a signature of excess glucose being released as lactate due to mitochondrial overload.

Case report: Resolution of malignant canine mast cell tumor using ketogenic metabolic therapy alone.

Background: Mast cell tumors (MCT) are common neoplasms in dogs and are similar to most other malignant cancers in requiring glucose for growth, regardless of histological grade. Ketogenic metabolic therapy (KMT) is emerging as a non-toxic nutritional intervention for cancer management in animals and humans alike. We report the case of a 7 years-old Pit Bull terrier that presented in 2011 with a cutaneous mast cell tumor under the right nostril. Methods: The patient's parent refused standard of care (SOC) and steroid medication after initial tumor diagnosis due to the unacceptable adverse effects of these treatments. Following tumor diagnosis, the patient's diet was switched from Ol'Roy dog food to raw vegetables with cooked fish. The tumor continued to grow on this diet until July, 2013 when the diet was switched to a carbohydrate free, raw calorie restricted ketogenic diet consisting mostly of chicken and oils. A dog food calculator was used to reduce calories to 60% (40% calorie restriction) of that consumed on the original diet. A total of 444 kilocalories were given twice/day at 12 h intervals with one medium-sized raw radish given as a treat between each meal. Results: The tumor grew to about 3-4 cm and invaded surrounding tissues while the patient was on the raw vegetable, cooked fish diet. The tumor gradually disappeared over a period of several months when the patient was switched to the carbohydrate free calorie restricted ketogenic diet. The patient lost 2.5 kg during the course of the calorie restriction and maintained an attentive and active behavior. The patient passed away without pain on June 4, 2019 (age 15 years) from failure to thrive due to an enlarged heart with no evidence of mast cell tumor recurrence. Conclusion: This is the first report of a malignant cutaneous mast cell tumor in a dog treated with KMT alone. The resolution of the tumor in this canine patient could have been due to the diet-induced energy stress and the restriction of glucose-driven aerobic fermentation that is essential for the growth of most malignant tumors. Further studies are needed to determine if this non-toxic dietary therapeutic strategy could be effective in managing other canine patients with malignant mast cell tumors.

Oxygen mass transfer enhancement by activated carbon particles in xylose fermentation media.

In this work, the effect of activated carbon particles on the production of xylonic acid from xylose by Gluconobacter oxydans in a stirred tank bioreactor was investigated. The enhancement of the oxygen transfer coefficient by activated carbon particles was experimentally evaluated under different solids volume fractions, agitation and aeration rates conditions. The experimental conditions optimized by response surface methodology (agitation speed 800 rpm, aeration rate 7 L min-1, and activated carbon 0.002%) showed a maximum oxygen transfer coefficient of 520.7 h-1, 40.4% higher than the control runs without activated carbon particles. Under the maximum oxygen transfer coefficient condition, the xylonic acid titer reached 108.2 g/L with a volumetric productivity of 13.53 g L-1 h-1 and a specific productivity of 6.52 g/gx/h. In conclusion, the addition of activated carbon particles effectively enhanced the oxygen mass transfer rate. These results demonstrate that activated carbon particles enhanced cultivation for xylonic acid production an inexpensive and attractive alternative.

Environmental sustainability analysis of dairy bedding regeneration system based on emergy evaluation and life cycle assessment methods.

Dairy farm bedding can be produced by composting technology using dairy manure, which offers advantages in terms of cost, availability, and economic value. However, few information is available on the environmental sustainability and impacts for manure recycling systems based on different composting methods. The resource-environmental impact and eco-economic sustainability of two manure bedding regeneration systems: forced-ventilation static-stack aerobic fermentation (FVSSAF) system (Scenario A) and bedding recovery unit (BRU) system (Scenario B) were evaluated in this study. The life cycle assessment yielded a combined environmental impact potential of 0.01032 for scenario B, much lower than the 0.02656 for scenario A. The emergy evaluation showed that scenario B can handle more dairy manure than scenario A due to 57% increase of emergy input. Form the emergy indices of the two systems, scenario B had lighter environmental pressure and higher sustainability. Therefore, the BRU system had economic advantages and ecological sustainability, which was more suitable for large dairy farms. The trade-offs between environmental consequences, resource efficiency, and economic benefits were analyzed from several perspectives in this study, which would help stakeholders to have a new understanding when choosing a bedding recycling system.

Cell wall ester modifications and volatile emission signatures of plant response to abiotic stress.

Growth suppression and defence signalling are simultaneous strategies that plants invoke to respond to abiotic stress. Here, we show that the drought stress response of poplar trees (Populus trichocarpa) is initiated by a suppression in cell wall derived methanol (MeOH) emissions and activation of acetic acid (AA) fermentation defences. Temperature sensitive emissions dominated by MeOH (AA/MeOH <30%) were observed from physiologically active leaves, branches, detached stems, leaf cell wall isolations and whole ecosystems. In contrast, drought treatment resulted in a suppression of MeOH emissions and strong enhancement in AA emissions together with volatiles acetaldehyde, ethanol, and acetone. These drought-induced changes coincided with a reduction in stomatal conductance, photosynthesis, transpiration, and leaf water potential. The strong enhancement in AA/MeOH emission ratios during drought (400%-3500%) was associated with an increase in acetate content of whole leaf cell walls, which became significantly 13 C2 -labelled following the delivery of 13 C2 -acetate via the transpiration stream. The results are consistent with both enzymatic and nonenzymatic MeOH and AA production at high temperature in hydrated tissues associated with accelerated primary cell wall growth processes, which are downregulated during drought. While the metabolic source(s) require further investigation, the observations are consistent with drought-induced activation of aerobic fermentation driving high rates of foliar AA emissions and enhancements in leaf cell wall O-acetylation. We suggest that atmospheric AA/MeOH emission ratios could be useful as a highly sensitive signal in studies investigating environmental and biological factors influencing growth-defence trade-offs in plants and ecosystems.

Efficient aerobic fermentation of gluconic acid by high tension oxygen supply strategy with reusable Gluconobacter oxydans HG19 cells.

Gluconic acid is a widely used food and beverage additive, but its production suffers from low efficiency and high cost. In this study, a preferable gluconic acid biosynthesis method without repeated seed culture was proposed and developed using the superior performance of Gluconobacter oxydans. A high oxygen atmosphere satisfying the demand of bio-oxidation increased the productivity of gluconic acid up to ~ 32 g/L/h and the accumulation up to ~ 420 g/L within 24 h of fed-batch fermentation. However, the productivity remarkably decreased when the gluconic acid content was over 350 g/L. Therefore, a continuous fermentation was designed, which in combination with 5 runs of fed-batch fermentation resulted in the final production of 1700 g gluconic acid from 1750 g glucose within 60 h in a 3 L bioreactor. The results suggest that the validity of this model and can enable cost-competitive gluconic acid production in the industry.

Insight to maturity during biogas residue from food waste composting in terms of multivariable interaction.

This study used biogas residue produced by anaerobic fermentation of food waste as the raw material in large-scale windrow composting. The effects of the addition of a microbial consortium on the physical and chemical properties and stability of composting of biogas residue were studied. The maturity of food waste biogas residue during composting was investigated by multivariate interaction of environmental, maturity, and nutrient parameters, using structural equation modeling (SEM). Results showed that the temperature of T2 compost with the microbial consortium increased more rapidly. The pH ranges of T1 (without the microbial consortium) and T2 were 8.75-9.15 and 8.42-9.27, respectively; the electrical conductivity (EC) ranges of T1 and T2 were 2.74-3.95 mS/cm and 2.81-3.85 mS/cm, respectively; the degradation rates of organic matter (OM) in T1 and T2 were 21.74% and 33.62%, respectively; and the total nitrogen (TN) ranges of T1 and T2 were 1.93-3.10% and 1.80-3.21%, respectively. By the end of composting, the germination indices (GI) of T1 and T2 were 20.57% and 64.24%, respectively. The total oxygen consumption after 4 days (AT4) was 1.88 mg-O2/g and 1.2 mg-O2/g in T1 and T2, respectively. SEM of T1 showed that compost temperature and EC were important factors affecting compost maturity. These factors highly significantly affected OM, which in turn affected AT4 of the biogas residue composting. SEM of T2 showed that compost temperature, pH, and EC affected OM, which in turn affected compost maturity. Temperature affected compost maturity by affecting AT4 and GI. Principal component analysis (PCA) showed that the overall score of T2 was higher than that of T1, indicating that the addition of the microbial consortium was beneficial for industrial-scale composting of biogas residue produced by anaerobic digestion of food waste.

Metabolic engineering of threonine catabolism enables Saccharomyces cerevisiae to produce propionate under aerobic conditions.

BACKGROUND: Propionate is widely used as a preservative in the food and animal feed industries. Propionate is currently produced by petrochemical processes, and fermentative production of propionate remains challenging. METHODS AND RESULTS: In this study, a synthetic propionate pathway was constructed in the budding yeast Saccharomyces cerevisiae, for propionate production under aerobic conditions. Through expression of tdcB and aldH from Escherichia coli and kivD from Lactococcus lactis, L-threonine was converted to propionate via 2-ketobutyrate and propionaldehyde. The resulting yeast aerobically produced 0.21 g L-1 propionate from glucose in a shake flask. Subsequent overexpression of pathway genes and elimination of competing pathways increased propionate production to 0.37 g L-1 . To further increase propionate production, carbon flux was pulled into the propionate pathway by weakened expression of pyruvate kinase (PYK1), together with overexpression of phosphoenolpyruvate carboxylase (ppc). The final propionate production reached 1.05 g L-1 during fed-batch fermentation in a fermenter. CONCLUSIONS AND IMPLICATIONS: In this work, a yeast cell factory was constructed using synthetic biology and metabolic engineering strategies to enable propionate production under aerobic conditions. Our study demonstrates engineered S. cerevisiae as a promising alternative for the production of propionate and its derivatives.

Study on personalized microbial formulation during high-temperature aerobic fermentation of different types of food wastes.

The rapidly growing generation of food wastes has attracted extensive attention. In this context, biochemical processors, using high-temperature aerobic fermentation, has become a beneficial method to treat food waste in situ. However, existing microbial agents do not vary the proportion of strains according to the different food wastes, with this approach affecting the degradation efficiency. In this study, high-temperature resistant strains, with high degradation efficiency, were isolated and screened, before establishing a novel method for preparing personalized microbial formulations. Using the degradation efficiency of wastes after three days as the evaluation standard, 12 groups of Plackett-Burman experiments were used to determine the main effect strains for different types of food waste. Fifteen groups of Box-Behnken experiments were then used to determine their best proportions at which the maximum degradation efficiency occurred. Finally, simulated fermentation experiments were used to check for improvement of the fermentation process by mixing strains according to the personalized proportions. Results of molecular identification and physiological assessments indicated that all the seven strains were Bacillus spp., with no antagonistic effects between them. Based on the Plackett-Burman and Box-Behnken tests, three personalized bacterial agents were obtained for different types of food waste. The fermentation results further showed that, compared with the use of equal proportions of strains, a maximum increase of 15.43% in organic matter degradation was achieved after adding personalized proportions. This study provides both theoretical and practical references for the use of personalized microbial agent formulations for high-temperature aerobic fermentation of food wastes, thus providing these microbial agents with good prospects and economic value.